African Journal of
Biotechnology

  • Abbreviation: Afr. J. Biotechnol.
  • Language: English
  • ISSN: 1684-5315
  • DOI: 10.5897/AJB
  • Start Year: 2002
  • Published Articles: 12191

Full Length Research Paper

Genetic diversity analysis in the Hypericum perforatum populations in the Kashmir valley by using inter-simple sequence repeats (ISSR) markers

Shazia Farooq
  • Shazia Farooq
  • Division of Floriculture Medicinal and Aromatic Plants, Sher-e- Kashmir University of Agricultural Sciences and Technology, Shalimar, Srinagar, J.K, India
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M. A. Siddiqui
  • M. A. Siddiqui
  • Division of Floriculture Medicinal and Aromatic Plants, Sher-e- Kashmir University of Agricultural Sciences and Technology, Shalimar, Srinagar, J.K, India
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P. C. Ray
  • P. C. Ray
  • Cancer Genetics Lab, Department of Biochemistry, Maulana Azad Medical College and Associated Hospitals, New Delhi, India
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M. Q. Sheikh
  • M. Q. Sheikh
  • Division of Floriculture Medicinal and Aromatic Plants, Sher-e- Kashmir University of Agricultural Sciences and Technology, Shalimar, Srinagar, J.K, India.
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Sheikh Shahnawaz
  • Sheikh Shahnawaz
  • Cancer Genetics Lab, Department of Biochemistry, Maulana Azad Medical College and Associated Hospitals, New Delhi, India
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M. Ashraf Bhat
  • M. Ashraf Bhat
  • Division of P.B.G, SKAUST, Shalimar, Srinagar J.K, AMU, UP, India
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M. R. Mir
  • M. R. Mir
  • Department of Botany, AMU, UP, India
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M. Z. Abdin
  • M. Z. Abdin
  • Dean, Faculty of Science, Jamia Hamdard, Hamdard Nagar, New Delhi-110062, India
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Imtiyaz Ahmad
  • Imtiyaz Ahmad
  • Cancer Genetics Lab, Department of Biochemistry, Maulana Azad Medical College and Associated Hospitals, New Delhi, India
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Jamsheed Javid
  • Jamsheed Javid
  • Cancer Genetics Lab, Department of Biochemistry, Maulana Azad Medical College and Associated Hospitals, New Delhi, India
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Prasant Yadav
  • Prasant Yadav
  • Cancer Genetics Lab, Department of Biochemistry, Maulana Azad Medical College and Associated Hospitals, New Delhi, India
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M. Masroor
  • M. Masroor
  • Cancer Genetics Lab, Department of Biochemistry, Maulana Azad Medical College and Associated Hospitals, New Delhi, India
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Mariyam Zuberi
  • Mariyam Zuberi
  • Cancer Genetics Lab, Department of Biochemistry, Maulana Azad Medical College and Associated Hospitals, New Delhi, India
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Alpana Saxena
  • Alpana Saxena
  • Cancer Genetics Lab, Department of Biochemistry, Maulana Azad Medical College and Associated Hospitals, New Delhi, India
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Rashid Mir
  • Rashid Mir
  • Cancer Genetics Lab, Department of Biochemistry, Maulana Azad Medical College and Associated Hospitals, New Delhi, India
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  •  Accepted: 23 October 2013
  •  Published: 01 January 2014

Abstract

Assessment of genetic variability among the Hypericum perforatum populations is critical to the development of effective conservation strategies in the Kashmir valley. To obtain accurate estimates of genetic diversity among and within populations of H. perforatum, inter-simple sequence repeats (ISSR) markers were used. The study was aimed to check, whether ISSR fingerprinting may be a useful tool for studying genetic variations among H. perforatum populations in the Kashmir valley (India). A total of 15 ISSR primers were tested with the 20 genotypes of H. perforatum. The ten informative primers were selected and used to evaluate the degree of polymorphism and genetic relationships within and among all the H. perforatum populations. ISSR of 20 genotypes analysis yielded 98 fragments that could be scored, of which 71 were polymorphic, with an average of 7.1 polymorphic fragments per primer. Number of amplified fragments varied in size from 150 to 1650 bp. Percentage of polymorphism ranged from 60% to a maximum of 100%. Resolving power ranged from a minimum of 7.7 to a maximum of 14.3. Shannon indexes ranges from 0.166 to 0.389 with an average of 0.198 and Nei’s genetic diversity (h) ranges from 6.98 to 9.8. Estimated value of gene flow (Nm = 0.579) indicated that there was limited gene flow among the populations. The genetic diversity (Ht) within the population of 0.245 was clearly higher than that of among population genetic diversity (Hs= 0.115), indicating an out-crossing predominance in the studied populations. Analysis of molecular variance by ISSR markers indicated that over half of the total variation in the studied populations (58%) could be accounted for by differences among the 8 divisions, with a further 42% being accounted for by the variation among populations within a division.The dendrogram grouping the populations by unweighted pair-group method with arithmetic averages (UPGMA) method revealed eight main clusters. In conclusion, combined analysis of ISSR markers and hypericin content is an optimal approach for further progress and breeding programs.

 

Key words:  Hypericum perforatum (St. John's Wort), inter-simple sequence repeats (ISSR) markers, unweighted pair-group method with arithmetic averages (UPGMA), Nei’s genetic diversity.

Abbreviation

Abbreviations: RAPD, Randomly amplified polymorphic DNA; RFLP, restriction fragment length polymorphism; AFLP, amplified fragment length polymorphism; ISSR, inter-simple sequence repeats; SSR, simple sequence repeat; Et-Br, ethidium bromide; PCR, polymerase chain reaction; ITS, internal transcribed spacer; Rp, resolving power; PIC, polymorphic information content; MI, marker index; Hav, average heterozygosity; EMR, effective multiplex ratio; DI,  diversity index; HPLC, high performance liquid chromatography.